For me, the references to the Givewell-approved charities and the lack of references to alternate existential risk reducing charities like FHI seemed to suggest that multifoliaterose was implicitly denying the existence of a third alternative. Perhaps EY read the post similarly.

I agree that this is the most probable meaning. The only other relevant consideration I know of is multi's statement upstream that he uses GiveWell in part to encourage transparency in other charities. Maybe he sees this as a way to encourage existential-risk charities to do better, making them more likely to succeed.